The range is a fault block of granitic rocks squeezed between the San Jacinto fault on the west and the San Andreas fault system on the east. The fault scarp on the northern and eastern side is one of the most abrupt in North America, going from sea level to 10,000 feet in a few miles. The height and steepness of the range points out that the San Jacinto fault and San Andreas fault are very active and very capable of producing major earthquakes (well in excess of magnitude 7). The last massive quake struck the southern segment of the San Andreas-San Jacinto fault complex more than 200 years ago making another major earthquake likely but not currently possible to predict. Rock slides from the range are possible during major earthquakes in the future, as they have been in the past. These slides may potentially impact the communities built directly adjacent to the steep escarpment on the desert side of the range.

The San Jacinto Mountains, like the neighboring San Bernardino Mountains, are a humid island above the surrounding desert and semi-desert. Annual precipitation ranges from about 15 inches at the western base (and only 6 inches on the eastern, desert base) to as much as 30 inches above 5,500 feet (the mountain town of Idyllwild averages 27 inches per year). The coastal (western) side of the range receives more precipitation than the eastern (desert) side. Most of the precipitation falls between November and March, with a secondary maximum associated with thunderstorms during the summer monsoon season between July and September. The precipitation totals are highly variable from year to year. Snow usually falls above 4,000 feet elevation in winter. Above 8,000 feet, snow sometimes persists until June. Near the crest, there are often a few patches of snow that may persist all year in shady spots.

The range can be thought of as a sky island, as it contains numerous species of flora and fauna that cannot tolerate the triple-digit-Fahrenheit heat of the surrounding valleys. Vegetation found on the mountain flanks is strongly influenced by elevation and climate. Near the valley floor, conditions are often arid and hot, limiting the vegetative palette to species that are adapted to such conditions.[4] At lower elevations forestation of the San Jacinto Mountains includes considerable California black oak associated with Coulter pine.[5] At higher elevations, forests include Ponderosa pine, Jeffrey pine, Lodgepole pine, Incense cedar, White fir, Red fir, and deciduous oak. There is also a grove of over 150 Giant Sequoia Trees on the northeast facing slope. The sequoias (native to the Sierra Nevada Mountains) were planted by the U.S. Forest Service in the 1970s, and are now apparently healthy and producing seedlings. [6] As in many other western U.S areas, bark beetle infestations have caused loss of some of the forest trees in recent years, especially during droughts. Wildfires have also temporarily denuded some areas.

Today, the range is a destination for outdoor recreation. The Pacific Crest Trail runs along the spine of the range. A popular walking route runs from the Palm Springs Aerial Tramway Mountain Station above Palm Springs, to the high point of the range, with a relatively mild climb of 2,400 ft (700 m) compared to other routes with more elevation gain.